The Japan Meteorological Agency (JMA) said a 30cm (1ft) tsunami was registered on the southern Nakanoshima island, part of Kagoshima prefecture.
There were no immediate reports of damage or injuries.
A tsunami warning issued for Kagoshima and Satsunan islands was later lifted. The quake happened at a depth of about 10km (six miles).
The US Geological Survey said it was some 159km south-west of the town of Makurazaki.
In 2011, a massive earthquake caused a tsunami that left more than 18,000 people dead or missing in north-eastern Japan.
Some 230,000 people have yet to return to their home towns since the disaster.